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- PDB-2vve: Crystal structure of the stem and receptor binding domain of the ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vve | ||||||
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Title | Crystal structure of the stem and receptor binding domain of the spike protein P1 from bacteriophage PM2 | ||||||
![]() | SPIKE PROTEIN P1 | ||||||
![]() | VIRAL PROTEIN / VIRAL STEM-RECEPTOR BINDING DOMAIN | ||||||
Function / homology | Jelly Rolls - #770 / Jelly Rolls - #720 / virion component / Jelly Rolls / Sandwich / Mainly Beta / Spike protein P1![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Abrescia, N.G.A. / Grimes, J.M. / Kivela, H.K. / Assenberg, R. / Sutton, G.C. / Butcher, S.J. / Bamford, J.K.H. / Bamford, D.H. / Stuart, D.I. | ||||||
![]() | ![]() Title: Insights Into Virus Evolution and Membrane Biogenesis from the Structure of the Marine Lipid-Containing Bacteriophage Pm2. Authors: Abrescia, N.G.A. / Grimes, J.M. / Kivela, H.K. / Assenberg, R. / Sutton, G.C. / Butcher, S.J. / Bamford, J.K.H. / Bamford, D.H. / Stuart, D.I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 223.3 KB | Display | ![]() |
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PDB format | ![]() | 179 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.8 KB | Display | ![]() |
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Full document | ![]() | 424.7 KB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 37.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vvdSC ![]() 2vvfC ![]() 2w0cC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 28591.408 Da / Num. of mol.: 2 / Fragment: STEM-RECEPTOR BINDING DOMAIN, RESIDUES 82-335 Source method: isolated from a genetically manipulated source Details: CLONED FRAGMENT STARTS AT RESIDUE 82 AND STOPS AT RESIDUE 335 Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.4 % Description: THE ELECTRON DENSITY MAP FOR THE STEM DOMAIN WAS GREATLY IMPROVED BY USING BUSTER PROGRAM IN THE EARLY REFINEMENT CYCLES |
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Crystal grow | pH: 8 Details: 7.3MG/ML (IN 150MM NACL, 20MM TRIS PH 7.5, 10MM CACL2),20%(W/V) PEG6K,100MM TRIS PH 8, 200MM LICL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 30, 2006 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9185 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→23 Å / Num. obs: 47548 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 30.2 |
Reflection shell | Resolution: 1.77→1.83 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.8 / % possible all: 71.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2VVD Resolution: 1.77→23 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.082 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DESPITE HAVING TWO MOLECULES IN THE ASU THE RESPECTIVE STEM DOMAINS FLEX WITH DIFFERENT ANGLES RELATIVE TO THE RECEPTOR DOMAIN. THEREFORE NO STRICT NCS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.65 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→23 Å
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Refine LS restraints |
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